cleaner code

SVN: 24724

deep_sequencing_unit/dist/etc/data-set-handler-alignment.py

@@ -9,15 +9,25 @@ TOTAL_READS, MAPPED_READS
 
 Obviously you need a working samtools binary
 
+Uses 'flagstat' and 'view -H'
+
 Note: 
 print statements go to: ~openbis/sprint/datastore_server/log/startup_log.txt
 '''
 
 import os
+import fnmatch
+import re
 from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
 
-FOLDER='/net/bs-dsu-data/array0/dsu/dss/incoming-jython-alignment/'
+FOLDER='/links/shared/dsu-dss/dss/incoming-jython-alignment/'
 SAMTOOLS='/usr/local/dsu/samtools/samtools'
+BAM_PATTERN='*.bam'
+
+matches = []
+searchStrings = ['@PG']
+programList = []
 
 # Create a "transaction" -- a way of grouping operations together so they all
 # happen or none of them do.
@@ -30,27 +40,76 @@ dataSet.setMeasuredData(False)
 incomingPath = incoming.getAbsolutePath()
 
 # Get the incoming name 
+# expected: 
+# Project_110907_SN792_0059_AC012FACXX_3/Sample_BSSE-DSU-1662/BSSE-DSU-1662_CGATGTA_L003_R1_001_sorted.bam
 name = incoming.getName()
-# expected incoming Name, e.g.:ETHZ_BSSE_110429_63558AAXX_1_sorted.bam
-split=name.split("_")
-sample=split[2]+ '_'+ split[3] + ':' + split[4] 
+split=name.split('_')
+if (len(split) == 6): 
+  incoming_sample=split[1]+ '_'+ split[2] + '_' + split[3] + '_' + split[4]+ ':' + split[-1]
+if (len(split) ==4):
+  incoming_sample=split[1]+ '_'+ split[2] + ':' + split[-1]
+
+
+# Looking for BAMS:
+for root, dirnames, filenames in os.walk(FOLDER + name):
+  for filename in fnmatch.filter(filenames, BAM_PATTERN):
+      matches.append(os.path.join(root, filename))
+
+# -----------------------------------------------------------------------------
+
+def listSearch (myList, searchString):
+  '''
+  Searches for a given String in a list.
+  Only lines matching  the start of a line a considerd as a match
+  '''
+  matches = []
+  for i in range (0, len(myList)):
+    if(re.match(searchString, myList[i])):
+      matches.append(myList[i])
+  return (matches)
+
+# -----------------------------------------------------------------------------
+
+def programParameters (programList):
+  '''
+  Extracts the aligner datils from the bam header
+  '''
+  elements = {}
+  for program in range(0, len(programList)):
+    line = programList[program].split('\t')
+ 
+  for element in range (1, len(line)):
+    key, value = line[element].split(":")
+    elements[key] = value
+    
+  return elements  
+
 
 # Extract values from a samtools view and set the results as DataSet properties 
 # Command: samtools view -H ETHZ_BSSE_110429_63558AAXX_1_sorted.bam
-arguments = SAMTOOLS + ' view -H ' + FOLDER + name
-#print('Arguments: '+ arguments)
+
+arguments = SAMTOOLS + ' view -H ' + matches[0]
+print('Arguments: '+ arguments)
 cmdResult=os.popen(arguments).read()
-properties=cmdResult.split("\n")[-2].split('\t')
-aligner=(properties[1].split(':')[1].upper() +  '_' + properties[2].split(':')[1])
-command=properties[3]
 
-arguments = SAMTOOLS + ' flagstat ' + FOLDER + name
+properties=cmdResult.split("\n")
+for s in range (0, len(searchStrings)):
+  programList = listSearch (properties, searchStrings[s])
+print(programList)  
+
+e = programParameters (programList)  
+
+dataSet.setPropertyValue("ALIGNMENT_SOFTWARE", e['ID'])
+dataSet.setPropertyValue("VERSION", e['VN'])
+dataSet.setPropertyValue("ISSUED_COMMAND", e['CL'])
+
+
+arguments = SAMTOOLS + ' flagstat ' + matches[0]
+
 cmdResult=os.popen(arguments).read()
 totalReads=cmdResult.split('\n')[0].split(' ')[0]
 mappedReads=cmdResult.split('\n')[2].split(' ')[0]
 
-dataSet.setPropertyValue("ALIGNMENT_SOFTWARE", aligner)
-dataSet.setPropertyValue("ISSUED_COMMAND", command)
 dataSet.setPropertyValue("SAMTOOLS_FLAGSTAT", cmdResult)
 dataSet.setPropertyValue("TOTAL_READS", totalReads)
 dataSet.setPropertyValue("MAPPED_READS", mappedReads)
@@ -63,8 +122,16 @@ search_service = transaction.getSearchService()
 
 # Search for the sample
 sc = SearchCriteria()
-sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, sample));
+sc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.CODE, incoming_sample));
 foundSamples = search_service.searchForSamples(sc)
 
 if foundSamples.size() > 0:
   dataSet.setSample(foundSamples[0])
+  
+  # Search for parent data set of the same sample
+  dataSetSc = SearchCriteria()
+  dataSetSc.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(SearchCriteria.MatchClauseAttribute.TYPE, 'FASTQ_GZ'))
+  dataSetSc.addSubCriteria(SearchSubCriteria.createSampleCriteria(sc))
+  foundDataSets = search_service.searchForDataSets(dataSetSc)
+  if foundDataSets.size() > 0:
+    dataSet.setParentDatasets([ds.getDataSetCode() for ds in foundDataSets])